I would feel better if there were "official" removal instructions from apple knowledge base! Or even better, a removal tool? Anything like that available?
Just do what arn said. It's pretty much the official removal tool.
PS:
It sounds like you are trying to throw away your OSX system folder. The folder labeled "System" is OSX, while the folder labeled "System Folder" is OS9.
You most likely need Administrator priviledges to remove the OS 9 system folder (I did). There's also other Classic components floating around in the OS X system folder such as the Classic preferences. I suggest doing a search on www.macosxhints.com